I'd like totake a swing at answering your questions one by one, from my point of view.
1) what is the purpose of the ppsc system?
It is a way to distribute the points invested by the players in a game. It's not inherently better than WTA, but it's not inherentely worst. Hence, the ability to choose between one or the other.
2) what benefits does it offer over a wta-only system?
Well, PPSC let's players be rewarded for a good game being played, even if they didn't end up on top. This is something that is usually a good thing, specially when the player is new to the game, or in other circunmstances such as a middle class player daring to play the top rankers. Wouldn't you want to reward that guy if he did a good job?
Also, it makes for players fighting things to the bitter end. If you survive with at least one SC, then you got something out of that game, as little as it may be. In WTA, when you know you can't win or force a draw, you've got nothing to play for except what you may consider honor... and many players (particularily the newer ones) don't seem to have much of that.
I know that you can describe the benefits for a WTA, that's why you like it, but PPSC has benefits that are neither better nor worse than WTA's, they're just different.
3) can we achieve those same benefits with a purly wta-system?
No, we can't. How could we? You call PPSC a variant, and I'm not completely disagreeing with that view (I would call both PPSC and WTA specific houserules to adress something the original game does not, wich is a ranking method). Can you create the same feeling as in a gunboat game but with people talking to each other privately?
If the answer is no, then you can't get the same things you get out of PPSC in WTA. Sorry.
4a) if so - how difficult is it to program?
4b) and how difficult will it be for the community as a whole to transition?
4c) if not - what other proposals can be made to cover those benefits without losing the wta nature of teh game?
I would say:
1 - Allow players to create WTA games as soon as they have finished a single game (No newbies creating WTA, as explained before, PPSC is best for newbies, but to be under 100 D does not make you a newbie).
2 - Display 4 sub-tabs in the Joinable Games tab:
a - WTA
b - PPSC
c - CD's
d - All of the above
With PPSC being the default shown for new players.
3 - Stop whining about what people do when you are not forced to join their games. You like playing WTA, you can play WTA, give the rest of us a break.